Charlie fears flying, so he is acutely nervous when he boards the plane for Chicago. He thinks about crashing, which leads him to reflect on the existence of God. He had always thought of Him as akin to Santa Claus. His mother believed in God, feared Him, and prayed to Him. Charlie’s father, however, thought of God as one of his wife’s relatives whom he did not want to associate with.

Charlie’s anxiety heightens when he is requested to put on his seat belt. He flashes back to an incident in his childhood when he was around five years old. His mother (and unwillingly his father) took him to a quack doctor who claimed to be able to cure Charlie’s mental handicap. Charlie was strapped down, so frightened that he messed his pants. Although the doctor promised him that he would become smarter, he never did. Charlie began to associate fear and shame with being strapped down. Following the birth of his sister, a "normal" child, Charlie’s mother did not worry about Charlie’s being “cured."

As Charlie enters the hotel where the convention is held, he reflects that Guarino, the quack doctor from his childhood, had at least treated him as a human being, something that Professor Nemur does not do. At the convention, Charlie feels more than ever that he is a lab specimen. The other scientists question him about numerous topics, all of which he addresses with depth and insight. When Charlie notices that Nemur is feeling angry and left out, he deflects a question concerning the type of retardation that Charlie had over to Nemur. When Nemur goes into great technical detail about the treatment, the other scientists lose interest. Charlie realizes that Nemur has not read the latest research on neuropsychiatry, especially that which relates to Charlie’s case. Charlie realizes that Nemur knows less about the brain than Charlie does.

As the presentation gets underway, Charlie’s resentment grows. He considers releasing Algernon from his cage. As Nemur presents his research, Charlie realizes that Nemur did not take into consideration the rate of increase when he predicted that Charlie’s increase in intelligence was permanent. Charlie realizes that, after all, he may slide back to his previous condition, perhaps into an even lower-level IQ. He realizes that the scientists did not understand what they had done. Charlie releases Algernon from his cage, causing mass panic. As everyone scrambles, trying to catch Algernon, Charlie finds him in the women’s restroom, takes him, and sneaks back to the hotel. He grabs his bags, uses his return ticket to go back to New York, where he takes lodgings in a hotel until he can make other arrangements.